We have explored transcriptional patterns associated with spontaneous cancer development and chemically-induced carcinogenesis. In these studies, it is necessary to control mixed directional false discovery rate due to the fact that we tested for multiple comparisons and there is a potential for directional errors when declaring genes to be up- or downregulated. Global gene expression patterns of tumors arising in response to the toxicant Vinylidene Chloride were compared to spontaneous mesotheliomas and F344/N rat mesothelial cells (Fred-PE) in order to discover the functions associated with VDC exposure. The data produced from VDC-treated animals suggested that exposure to this asbestos-related chemical is associated with the gene regulation of oncogenes, growth factors, and cell cycle response (Blackshear et al., 2014). A separate study addressed whether gene expression changes in human blood cells differ between individuals who are resistant or sensitive to sleep deprivation. We found that two genes (SREBF1 and CPT1A, associated with lipid metabolism) held small changes over time during sleep deprivation. We also found a reduction in amplitude of normally cycling transcripts due to sleep deprivation which was higher in resistant subjects compared to sensitive subjects (Arnardottir et al., 2014). Another study examined the dynamic expression of prion-like proteins in the pharynx of Caunorhabditis elegans. The grinder, a tooth-like specialization to crush food, lies at the posterior end of the pharynx. To study the structure of the grinder and pharynx cuticle, we examined the gene expression response during the molt. The results identified abu genes encoding prion-like proteins that were induced during the molt. Abnormal cuticle function resulted from knocking down genes in the abu/pqn paralog group. Transcriptinoal studies without precise staging might inappropriately find changes in these genes since they are strongly regulated during development (George-Raizen et al., 2014).